The Take Over
by Loki'sArmy0602
Summary: "Log number 31. The date is July 6th, at… 23:43. The last of S.H.I.E.L.D is down, it's gone. They have Captain America, Agent Romanoff and Doctor Bruce banner... Two months of nearly no food or water for all America. HYDRA is at the rise and no-one can stop them," They knew that the day would come and it did. The day it all started. The day everyone's lives were destroyed by HYDRA
1. Chapter 1

"Log number 31. The date is July 6th, at… 23:43. The last of S.H.I.E.L.D is down, it's gone. They have Captain America, Agent Romanoff and Doctor Bruce banner…They've took them. Two months of nearly no food or water for all America. HYDRA is at the rise and no-one can stop them," Tony said. The camera moved, un-focusing and then focusing on his face again. Blood dripped down from the cut on his forehead and down his cheek. The lighting around Tony's face was dark as he sniffed. Tony's breathing was heavy and his eyes were blood shot and wide. He turned his head to look behind him, hair sticking out in different directions. He looked panicked and on edge. Anxious. He turned back around to face the camera. He looked tired, his face nearly taking up the whole screen.

"I repeat no-one can stop them. Stay under ground people... Don't be the hero... it's foolish to thing you, only you, can defeat them. So stupid," Tony muttered the last bit to himself. He shook his head to concentrate and looked back at the camera. He sniffed again. "Food supplies are hopefully coming from the US and the UK Army, but do not get your hopes up. Not everyone will get some. Ration your food, don't waste it. HYDRA are strong, their powerful. I repeat stay. Under. Ground." Tony sniffled again and then coughed. There was a bang behind him and Tony's head snapped around to look behind him. He quickly turned around to look at the camera again, words rushing out.

"Stay hopeful America..." Tony Stark said yet he seemed to think that it was the end. "This is... This was Tony Stark saying his last words to you. Peace guys. Over and out," Tony said before the screen went blank.

Everyone stared at it in shock.

Many people in the underground train track huddled together as the loud explosion occurred above them. People also huddled together in and out of the abandoned train on the tracks. Lights flickered along the track, giving a kind of horror movie feeling. Someone started to cry to the right of the underground train track, causing someone else to go over to them, placing an arm around their shoulder. They didn't know each other but everyone needed someone to be there for them.

Pepper looked at the blank screen as another loud explosion went off above them, making many people around her flinch and cry out in terror. Dust fell from the curved ceiling that ran down to the track floor. A man at the back of the group started to cough. Pepper turned away from the blank screen taking a deep breath.  
>This is worst then the alien invasion. Worst than the Mandarin, pepper thought.<p>

This was it.

Nothing was ever going to be the same again.

Pepper turn on the comm link that was in her ear. She had turned it off after a loud ear piercing sound had rang through it before Tony had broadcasted the video worldwide. The comm link was to stay in touch with Hill and Barton. However she hadn't heard a word from them before she had turned the comm off. She had lost touch with them about twenty minutes ago. They had both stupidly gone off down the train track, alone, to try and find anyone or anything that could help them.

Pepper sat down on the side of the train track as another explosion went off, causing many more people to start to cry and dust fall from the curved ceiling once more. Pepper listened down the comm for anyone as her boyfriends words sunk in.

Steve had been taken.

Natasha.

Bruce.

They were going down, one by one. She had no idea where Thor was. She hadn't heard from the God for a month now. Coulson and Fury, both disappeared about a month ago too. She hoped that Jane, Darcy and Betty were somewhere safe underground. Rhodes was up on the ground with the USA Army, fighting with everything he had against HYDRA. Nearly everyone at SHIELD who had been trusted had turned HYDRA. People within SHIELD who were HYDRA had killed many on that day. That day of the uprising of HYDRA. Hail hydra would be heard above them every so often and it just drained and drained the spirits of the people down here with Pepper. It had been one month and two weeks since everyone went underground. They had had to leave there last site after HYDRA had found them, killing many people within the group, making it down to around forty people in this group.

Clint had placed ten women and men around the little camp they had going on to stand guard. Each one had a SA80 assault rifle in their arms. The ten people after five hours would switch with another ten people so they could get some rest. Jarvis had been disconnected from nearly everything except the comm link. She could still talked to him, but he wasn't as "powerful" as normal. He couldn't find anyone, couldn't trace. Couldn't hack. The most Jarvis could do was be there and talk.

"...p-p-per," a voice came down the comm line. It crackled a little but it was hope. Pepper straighten up and people sitting near her noticed, turning to look at her.

"Maria?" Pepper asked, her finger going to press against the ear piece in her ear. It didn't help but it was just something Pepper had gotten used to doing.

"Pep-p-per," Maria voice came cracking down the comm link. "We f-found mo-r-re food." Maria said. This was the best news she had heard in a long time.

"It's all j-junk-kkkk-k food-d," Clint added down the line.

"Get back here now," Pepper said, her voice firm, standing up as she spoke. She wondered if they had heard since it took them a while the reply.

"B-be there s-sss-soon-n," Maria said.

"Over and o-out," Clint said.

"Over and out," Pepper replied. More people were looking at her now, hope in their eyes.

"Are they ok?" A women around mid thirties asked.

"They have food," Pepper said and everyone sighed in relief, a smile appearing on some of the sea of faces. Pepper turned to the right after hearing a sniffle to see Bethany, a six year old girl, curled up in a ball with tears running down her face. Pepper walked forward and sat down next to the young girl, pulling her into a hug.

"You're safe Bethany," Pepper said. The girl had lost her mother and father that day it had happened.

Around thirty minutes later, according to Pepper's very slow watch on her wrist, they heard footsteps coming down the track. Most people stood up and the five guards on the right lifted up their guns. Five on the right, five on the left, blocking the group in for safety reasons.

Two figures came walking toward the group. It was hard to tell who it was since the lighting in the under ground train track was very dark. The temperature slowly lowering and lowering.

"Don't shoot," Clint's voice echoed towards them. Pepper walked forward to stand in front of the group. She saw Maria and Clint come walking towards them. Clint however was limping, one arm around Maria's shoulder as she helped him. Maria had her deep blue rucksack hung over her left shoulder, Clint next to her on her right. She was supporting a bleeding head wound and two gun shot wounds. One a flesh injury the other one hitting her left arm, which she ignored the pain. Clint had come off worse, a stab wound to his right leg and three gunshot wounds. Pepper saw that both were covered in dust and dried blood. They looked like a train reck.

"I like you hair," Pepper called out to them.

"The Hulk cut it for me," Maria and Clint both replied at the same time. Pepper and the rest of the group relaxed a little. Pepper then rushed forward with four other people. Pepper took hold of Maria, handing the rucksack off to one of the people. Three people helped Clint get sat down inside the subway train were they had one medical kit between the forty of them. Maria sat down on one of the plastic red seats with Pepper sitting down next to her. Maria gestured to the man who took her rucksack to hand it to her. The man gave it to Maria and she opened it up.

"We got everything we could get from the vending machine before the HYDRA dumbasses ambushed us," Maria explained as one of the two doctors that was in the group cleaned her up, the other cleaning Clint up, who laid on the plastic chairs opposite the two women.

"We got out and managed to give them a false trail," Maria said and Pepper nodded, taking a deep breath.

"Tony... He erm... He updated," Pepper said and Maria looked up. Clint turned his head to look at them.

"What did he say?" Maria asked and Pepper looked down.

"That HYDRA are too strong and that we should stay underground. He said that Steve, Nat and Bruce had been taken. He said it was his... His last words," Pepper whispered. Maria wasn't big on hugs but realised the blonde really needed one. She placed her right arm around Pepper's shoulder and pulled the women towards her, holding her close.

"We'll find him," Maria told her, even though she didn't believe her own words. She didn't believe one word of them in fact. Pepper nodded, knowing Maria was only saying that to make her feel better. The doctor called Scar, finished cleaning up Maria and went to help the other doctor, called Raj, clean up Clint and stop him for bleeding so much.  
>The carriage they were in was empty except them, everyone leaving the doctors to do what they can do. Pepper closed her eyes as Maria hugged her, her heat beating strong after everything that had happened.<p>

"I'm sorry," Pepper said and Maria frowned, wondering what the women was talking about.

"Why?" Maria asked and Pepper pulled away to look at the brunette.

"You must be so upset," Pepper said. "Steve's been taken. I could see that you two loved each other, even though you both never said it," Pepper added. Maria took a deep breath.

"Like I said two days ago... It's going to be alright," Maria said, as Pepper looked into her blue eyes. She smiled lightly and pulled Maria into a hug.

It had all happened on May 29th 2015. The time had been 14:44. Weather was sunny with a chance of rain and the temperature was 26 degrees Celsius. It was that day... That day when it all happened. It was supposed to be a normal day in New York. But HYDRA decided that it was the day to take over.


	2. Chapter 2

*Two months ago*

At first it was only a few suspicious events here and there. One or two people dead, a couple robberies and a few HYDRA "take overs" in some parts of America. Nothing SHIELD couldn't handle. But it changed. Things got worst. More people died and the press were on it straight away, making it harder for S.H.I.E.L.D to cover up.

The bridge connecting New York with main America was full of cars. The news reporter on the radio that each car was listening to was telling them to evacuate New York City, or if it was too late and the battle had already reached them, the news reporter told those people to stay indoors. Underground if possible.

One little brunette girl, leaned out of the window to look back at New York. The men had come with robots and guns firing. Explosion's going off everywhere.  
>"Bethany, stay in the car," her very concerned mother said, gently grabbed onto her coat jacket and pulling her into the car. Bethany sat back in her car seat, pulling her brown fluffy bear that she had dressed like Captain America to her chest. The reporter started to talk about how the Avengers and S.H.I.E.L.D were tackling the situation. Bethany closed her eyes, squeezing her Captain America bear tighter.<p>

"Finally," her farther breathed as the car in front of them started to move. It seemed like they were finally getting to move, yet it was too good to be true. There was a loud explosion from above them. The cables spanned and the bridge shook. Car horns started to beep and people screamed inside their cars as another explosion occurred below them.

HYDRA was blowing up the bridge.

Bethany's father quickly turned around to unfasten Bethany from her car seat. He then turned and undid his seat belt, her mother following. People were running past each other on the bridge, people heading back to New York since it was the closest to where they were and then some people risked it, running for main land America. Bethany's hand slipped out of her mother's as someone ran into her, making her fall to the ground. There was a loud explosion underneath her and she felt the ground shake. She pulled herself up as the bridge cracked in the middle. She screamed as her mum and dad and many others fell off the bridge as it collapsed. The bridge was falling; Bethany turned and ran with the crowd, back to New York. The place she was still calling home. Her Captain America teddy bear still pinned to her chest as she ran.

*present day*

Maria walked over and sat down on the subway train's floor, Clint's head at her left shoulder. He was still laying on the red plastic chairs, half asleep.  
>"We need to find them," Clint mumbled to Maria, opening his eyes to look at the women. Maria sighed and rubbed a hand through her hair which she now never tied up since she had no grips. It hung lose, just past her shoulders.<p>

"I know," Maria said and then turned to look at Clint. "You need to eat," she said lifting up a chocolate bar she had in her pocket.

"Give it to someone else," Clint said and Maria sighed.

"You need to get back to strength Barton," Maria told him and it was his turn to sigh. He slowly sat up and Maria turned her whole body to face him. He took the chocolate bar from Maria as she got up to sit next to him.

"How's the leg?" Maria asked as Clint ripped the chocolate bar wrapper open.

"Feels like I got stabbed," Clint joked, trying to make light of a difficult time. Maria let a smile crack on her face as Clint bit into the chocolate bar and then moaned.

"It's chocolate, not sex," Maria commented and Clint just gave out a louder moan. Maria rolled her eyes and leaned back in the plastic seat, back of her head resting against the cool glass window.

"How long do you think..." Maria began to ask but couldn't finish. They had had this conversation on nearly a daily basis. Just to see if the other had changed their minds about how long it will be until they escape this shit hole.

"How about... in two days," Clint told her and for a second Maria thought he was kidding. However, when she looked over at him, away from one of the posters on the subway train wall that was slowly peeling away, she saw seriousness shine from him.

"You're not kidding, are you?" Maria asked.

"No we need to get out of here," Clint said. "There must be a computer room in this place. It is a train station after all," Clint said. They hadn't had enough time to be able to scout the place out yet. The last place they had set up camp, they hadn't had much communication with the outside world. Maria picked up on his line of thought straight away.  
>"We could get a message out to someone, Fury, Coulson... Tony possibly," Maria said, in hopes that Tony wasn't dead. Clint sighed and leaned back, rubbing his eyes. He threw the empty chocolate wrapped onto the floor.<p>

"We at least need to try. But this time it'll not just be me and you, get Pepper and the other people on guard to come," Clint said and Maria nodded.

"They know how to use a gun," Maria said and Clint hummed in reply.

"How are you feeling?" Clint asked her after a couple minutes of comfortable silence.

"I'm ok," Maria replied to Clint and he knew that was her way of saying she wasn't and she was scared for her life, Steve's life, everyone she trusted, everyone in their group right now. "You?"

"Me? Oh I'm doing great," Clint replied and Maria knew it was his way of saying he wasn't fine and wanted to find Natasha as soon as possible. Maria placed her head on Clint's shoulder and he brought an arm around her, pulling her into a side hug. He rested his head on hers and took a deep breath.

"I couldn't get through this without you by the way," Maria mumbled out after a while.

"I couldn't do it without you Maria," Clint said back to her. They had a friendship that ran so deep. They had been there for each other through thick and thin, missions and memories to share. Happy and sad. Clint kissed her on the hair; she was the sister he never had and he the brother she never had.

"You get some rest. Two days is when we start," Maria said, lifting her head up to look at him.

"Start what?" Pepper asked Maria, as the blonde walked into the subway cart.

"The take back."


	3. Chapter 3

He sure hoped Tony had survived. He couldn't bare see that man dead. Tony's blood would be on his hands. He was the leader after all, he had to look after his men... And Tony was one of them, even though the man insisted they weren't soldiers.

Steve shivered slightly as he hung from the metal chains. His muscles ached and his head spun. Only minutes ago was he and Tony trying to get Nat and Bruce out. They had found Bruce... But in a very bad state. The man was curled up in a ball in the corner of a brightly lite room. Ripped clothes surrounded him, his trousers hung loosely around his hips. The doctor had had a green hinge to his skin and bloody cuts running all along his body. Shivering violently.

Steve and Tony was so shocked at the state of him that they had paused. That little pause caused them, well Steve, to be captured. He hoped Tony had got out. The last thing he saw was Tony being chased down the corridor by about six men. Stark clearly wasn't having a fun time. They hadn't gotten Bruce out and hadn't even found Nat. The mission had failed, badly.

Steve let a loud breath as he swung slowly in the middle of the dimly lite room. He heard an explosion above him and dust fell from the ceiling, which was starting to cave in slightly. Steve pulled at the chains, trying to get free. However he couldn't. He had lost a lot of energy throughout the day. First fighting with about twenty drones with Tony, who didn't even have his suit anymore. HYDRA had gotten hold of his suits and were using them against the avengers and S.H.I.E.L.D.

S.H.I.E.L.D, that wasn't even a thing anymore. He had no idea where Maria was. His heart ached for her and prayed that she was alive somewhere underground, safe and alive that was all he asked God for. Yet she probable was out there kicking HYDRA's ass if he hadn't insisted she find safety before everything fucked up. He knew Maria wouldn't just sit around waiting to be saved. He missed her. He wished he had told her that he loved her because that chance may not come again.

No Clint, no Pepper, no Coulson or Fury. Everyone was gone.

The last thing that Thor had said was that he had to go deal with Loki, who apparently hadn't died and was fucking things up in Asgard. He respected that the god had his own things to deal with. Adopted not so dead brother turns evil and tries, and is succeeding at taking over the thrown... Yeah, the god had a lot on his plate.

Tony had been doing video logs that aired to all of America and other parts of the world, such as England and China. Tony had hacked into the computers and TV's, everything with a screen to send these videos out to the public. All to ensure people that everything was ok and to keep under ground. Also to inform everyone of everything they, Tony and Steve, knew. They had been the only thing that informed the public. The government was in ruins and HYDRA was everywhere. It was Steve's worst nightmare and it had all come true.

He had fought with Bucky and the rest of the howling commandos to get rid of HYDRA. He had even given his life to save everyone. Twice in fact.

It seemed now that everything Steve had fought for in World War Two was useless, since HYDRA had gained what it wanted.

He pulled again at the chains and slumped in defeat. He needed to get out... But how?

Slamming the camera shut and stuffing it into his ripped jeans pocket, Tony spun around to look for an escape. Finding the door and the vent. Tony went for the vent. It was the easiest option. I mean, he didn't want to face about twenty HYDRA agents at this moment in time. Not when the only weapon he had was the glock 47 hand gun, probably not even fully loaded.

He couldn't shake the image out of his head. His best friend laying there defenseless. He should have acted faster. He shouldn't have stopped. He wouldn't be in this position right now. He climbed higher up the vent, in hopes for some escape. Maybe he could go on top.

Bad idea sir, I would suggest under ground train stations, a voice said in head which sounded awfully like Jarvis. Tony missed his buddy, J.

He pulled himself to the right at a crossing, clawing along the vent for a bit and then laid down on his back. He needed to think. Good job his wasn't claustrophobic, he thought with a huffed laugh. He stared up at the sliver vent, thoughts running through his messed up head. The one that stood out the most was, go to Pepper. Tony closed his eyes and rubbed them until funny patterns started to appear. He blinked them back open as he heard the sound of HYDRA agents shouting.

"Shit, can't let a man rest can they," Tony mumbled to himself and rolled onto his front, army crawling through the vent. He came to a grate, hoping he could climb out of it to safety. However, he came across another member of his team.

Natasha.

She curled up in the corner of the room, head duck down low, arms wrapped around her head, knees brought up close to her body. She was so still Tony thought for a second she was dead, until her shoulders slowly moved, showing she was breathing. Still, but breathing. Her body showed no sign of injure except a little bit of dried blood within the parting of her hair. So no physical damage.

Mental damage. Yes.

Tony glanced around the room, finding one wall was a mirror, ceiling to floor. A brown wooden bar, ballet bar, ran across the middle of the mirror. The mirror had a smash with blood on it, like someone had smashed Natasha's head against it. The rest of the room was lite just enough to be able to see yourself in the mirror. No bed, no toilet. Just a mirror, another three grey concrete walls and a light bull hanging from a white cable over the room.

Tony glanced behind him as one of the HYDRA agents that had followed him into the room shouted, "He's escaped through the vents! Which dumbass is responsible for not locking the vent gates, fucking idiots!"

Tony then looked back at Natasha.

"Psst!" Tony whispered loudly. Natasha didn't move from where she was curled up, not even a twitch of a finger.

"Natasha. Psst, Nat," Tony whispered. Still no reply.

"Nat, fucking look at the vent gate you dick," Tony whispered louder this time. Natasha's head slowly lifted up and she glanced up to the vent gate, eyes narrowing. She seemed to not recognize him for a couple of seconds, but then everything clicked together and her eyes went back down to the ground. Tony frowned slightly.

"What's th-" Tony began to ask but then spotted it. He hadn't seen it a minute ago but now he saw the camera just above her. The red light blinking. Tony lent away from the vent gate, as Natasha slowly stood up, she had sat perfectly so that she wasn't seen by the camera. She then glanced up at the gate before looking up at the camera. She reached up and moved the camera so slowly that the people watching her won't notice if they weren't paying full attention. After she had moved the camera enough that the vent gate wasn't in sight and that it didn't reflect from the mirror, Natasha moved over to stand below it. Tony then got to work with kicking the gate open.

The bolt's loosen, with one last hard kick the gate fell off and Natasha caught it, silently placing it on the ground. Tony held out both his hands and Natasha took them without hesitation. Tony helped Nat walk up the wall to then be able to fully climb into the air vent. The second she was fully in the vent she collapsed onto Tony. He froze for a second as Natasha wrapped her arms around him, pulling him into a hug.

She had never shown so much emotion in front of him, but slowly Tony relaxed and hugged Natasha back.

"Not really into hugging," Tony mumbled as Nat closed her eyes.

"Thank you," she whispered, her voice cracking slightly. She then pulled away as Tony looked at her with shock. "We need to move. Now." Natasha said as loud shouts echoed from behind them where Tony had been. Tony nodded and then turned, crawling along the air vent.

"You ok?" Tony whispered to her.

"Fine," was her blunt reply. Tony knew she wasn't. They needed to get somewhere safe before Natasha fully cracks inside.

They had mentally tortured her, having not laid a finger on her except for when they smashed her head against the glass mirror. Memories of her past, which she had been able to push back, were pulled back torturing her for what she had done.

The ballet bar was just a small amount of what had happened to her. Word abuse was one of the things they had done to her, nearly 24/7. Bringing up memories of her past. The people she had killed, the pain she had caused. She was no hero, no good deed could make up for all of what she had done.

Tony started to climb up the ladder at the end of the vent and Natasha followed, staying silent throughout their escape. They finally made it out of the HYDRA complex in New York.

"Under ground," Tony mumbled to himself looking around where they were. He tried to remember how he had got from the subway station to the HYDRA complex with Steve.

Tony found the way to the subway and sat down on the tracks after they had walked for a while. Natasha sat opposite him, pressing her back against the wall. Tony studied her as she tried to look anyway but directly at him.

"You got a phone?" Natasha asked and Tony shook his head.

"I have a camera," Tony said. "I've been broadcasting to the world. Telling them what was going on and where to go to stay safe." Tony informed her.

"Smart," Natasha said. "You got any food?" Natasha asked him after a while. Tony reached into his pocket and pulled out a melted mars bar.

"It's the only thing I have," Tony said tossing it towards her. It landed next to her and she picked up, nodding thanks to him. After she finished it, she placed the wrapper onto the floor next to her.

"Have you heard anything from the others?" Natasha asked.

"The last thing I heard was that Steve's been captured, totally not my fault. Bruce is still back there... Thor's nowhere to been seen, much like Fury, Coulson, Sam... Pepper too. Maria was told by Steve to go to safety under ground, so she might be around somewhere," Tony gestured around him. "And Rhodey is working with what's left of the military." Tony finished off.

"Clint?"

"A no show too," Tony confirmed. Natasha looked away from him, down the train track to her right.

If only she knew Clint was only five miles away from her.


End file.
